fix: python (#158)

* fix: removed superflous conditional

* fix: bcftools seemed missing in environment.yaml

* feat: added seaborn to environment.yaml

* feat: new python rule demonstrating the run directive

* feat: added Snakefile to illustrate the python run directive and a solution

* feat: introducing the parson problem

* feat: extended reach of the Python section's scope

* fix: typo

* fix: added pip install of pysam to environment yaml file

* fix: 06_Snakefile_run task setting now syntactically correct

* feat: new slide introducing the Parson problem from the last commits as a task

* feat: added results positions file to illustrate the solution

* fix: removed outdated solution file 06

* fix: added filnalized version of for the run directive

* feat: no cloze for 07 script, but a solution

* feat: plot quals to rule creation, only discussing script in the future

* fix: bcftools with minimum version

* fix: removed doubled bcftools entry

* feat: added exercise to move run to script content

* fix: typo

* fix: grammar

* fix: layout glitches

* fix: layout (tabs to spaces)

* fix: a little clearer message

* feat: added dummy chapter entry for parallel execution chapter!

* fix: added missing source information

* fix: the suffix 'tex' for the editorfile lead to miscounting of the render script

* fix: clarification in sourcing bashrc

* fix: env creation was idented

* fix: line wrap problem when demonstrating minmum cluster software

* fix: remove suggestion to save, as everything is copied

* fix: removed braces in sentence - better layout

Author: cmeesters

config/config_Mainz_NHR.yaml

@@ -29,7 +29,7 @@ course:
   # Editors recommendations are a matter of taste and technological
   # setups (e.g. on-demand setups). Hence, specify an editor-slide,
   #  here:
-  editorfile: "common/mod_cs_mainz.tex"
+  editorfile: "common/mod_cs_mainz"
   # The next line indicates the slides explaining
   # a condarc file on a cluster, copy and adjust
   # for your cluster.

config/config_for_github.yaml

@@ -29,7 +29,7 @@ course:
   # Editors recommendations are a matter of taste and technological
   # setups (e.g. on-demand setups). Hence, specify an editor-slide,
   #  here:
-  editorfile: "common/editor_gedit_mainz.tex"
+  editorfile: "common/editor_gedit_mainz"
   # The next line indicates the slides explaining
   # a condarc file on a cluster, copy and adjust
   # for your cluster.

setup_creators/environment.yaml

@@ -20,4 +20,3 @@ dependencies:
     #  using pip
   - pygments
   - seaborn
-  

setup_creators/solutions/08_Snakefile_script2

@@ -1,6 +1,7 @@
 # our samples are pre-configured
 SAMPLES = ["A", "B"]
 
+configfile: "config/config.yaml"
 
 rule all:
     input:

setup_creators/solutions/09_Snakefile_config

@@ -1,3 +1,6 @@
+# our samples are pre-configured
+SAMPLES = ["A", "B"]
+
 configfile: "config/config.yaml"
 
 rule all:
@@ -38,8 +41,8 @@ rule samtools_index:
 rule bcftools_call:
     input:
         fa="data/genome.fa",
-        bam=expand("sorted_reads/{sample}.bam", sample=config["samples"]),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=config["samples"])
+        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
     output:
         "calls/all.vcf"
     shell:

slides/Snakemake_HPC_User_Creator_Combi.tex

@@ -89,6 +89,9 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{creators/Workflow_Parameterization_for_HPC}
 <+++ if course.question is defined +++>\include{common/question_time}<+++endif+++>
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\include{creators/Parallel_Execution}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{common/Reports}

slides/common/Why_Workflows.tex

@@ -27,7 +27,7 @@ \section{Why Workflows}
    \end{question}
    \begin{docs}[Objectives]
    	  \begin{enumerate}
-         \item Introducing workflow engines (particularly \Snakemake)!
+         \item Introducing workflow engines - particularly \Snakemake!
       \end{enumerate}
    \end{docs}
 \end{frame}  

slides/common/against_frustration.tex

@@ -3,7 +3,7 @@ \section*{Frustration}
 {   
 	\usebackgroundtemplate{
 		\vbox to \paperheight{\vfil\hbox to \paperwidth{\hfil\includegraphics[height=\paperheight]{humor/DALLE_frustration_to_heureka.jpg}\hfil}\vfil}
-		% source: https://en.m.wikipedia.org/wiki/File:Text-x-python.svg
+		
 	}
 	\frame{
 		\frametitle{Before we begin \ldots}
@@ -18,5 +18,6 @@ \section*{Frustration}
 				\item just a reason to ask
 			\end{itemize}
 		\end{mdframed}
+	    \vfill\hfil \hfill{\tiny image: own creation with DALL-E}
 	}
 }

slides/common/software_environment.tex

@@ -271,12 +271,10 @@ \subsection{Using Conda}
 \begin{frame}[fragile]
   \frametitle{Initializing Conda \& Mamba}
   To initialize Conda, simply run
+
   \begin{lstlisting}[language=Bash, style=Shell]
-$ bash
-  \end{lstlisting}
-  or (better)
-  \begin{lstlisting}[language=Bash, style=Shell]
-$ source ~/.bashrc
+$ # only once - not necessary after new login
+$ source ~/.bashrc 
   \end{lstlisting}
   Subsequently, run: 
   \begin{lstlisting}[language=Bash, style=Shell]
@@ -395,7 +393,7 @@ \subsection{Using Conda}
 	\frametitle{\HandsOn{Activating Environments}}
 	It is time to activate a shared environment:
 	\begin{lstlisting}[language=Bash, style=Shell]
-		$ mamba activate <<++course.softwarepath++>>
+$ mamba activate <<++course.softwarepath++>>
 	\end{lstlisting}
 	Your prompt should now feature the name of the environment: \altverb{snakemake}.
 \end{frame}

slides/creators/A_First_Workflow.tex

@@ -314,7 +314,6 @@ \subsection{A first Step or ``Rule''}
     \bcattention Python will concatenate those Strings! Be sure to include spaces to make up a valid command in Bash.
   \end{onlyenv}
   \begin{onlyenv}<5| handout:1>
-   Be sure to have copied everything to your \altverb{Snakefile} and save it.
    \begin{lstlisting}[language=Python,style=Python]
 rule bwa_map:
     input:

slides/users/Selecting_Workflows.tex

@@ -92,8 +92,9 @@ \subsection{The Snakemake Workflow Catalogue}
 	\frametitle{Deployment II - Creating an Environment Fork}
 	Usually, we can create an environment like:
 	\begin{lstlisting}[language=Bash, style=Shell]
-$ mamba create -c conda-forge -c bioconda -n snakemake snakemake \
-> snakemake-executor-plugin-slurm snakemake-storage-plugin-fs
+$ mamba create -c conda-forge -c bioconda -n snakemake \
+> snakemake snakemake-executor-plugin-slurm \
+> snakemake-storage-plugin-fs
     \end{lstlisting}
     This should install a \Snakemake{} environment with all necessary tools!